Mercurial > repos > iuc > package_augustus_3_1

changeset 0:cc0bd4986b48 draft

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Imported from capsule None
author iuc
date Fri, 22 May 2015 04:54:43 -0400
parents
children 5f78108125fd
files tool_dependencies.xml
diffstat 1 files changed, 33 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Fri May 22 04:54:43 2015 -0400
@@ -0,0 +1,33 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="augustus" version="3.1">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">http://bioinf.uni-greifswald.de/augustus/binaries/augustus-3.1.tar.gz</action>
+                <action type="shell_command">make</action>
+                <action type="move_directory_files">
+                    <source_directory>bin</source_directory>
+                    <destination_directory>$INSTALL_DIR/bin</destination_directory>
+                </action>
+                <action type="move_directory_files">
+                    <source_directory>scripts</source_directory>
+                    <destination_directory>$INSTALL_DIR/scripts</destination_directory>
+                </action>
+                <action type="move_directory_files">
+                    <source_directory>config</source_directory>
+                    <destination_directory>$INSTALL_DIR/config</destination_directory>
+                </action>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/scripts</environment_variable>
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                    <environment_variable name="AUGUSTUS_CONFIG_PATH" action="set_to">$INSTALL_DIR/config</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>AUGUSTUS is a gene prediction program for eukaryotes written by Mario Stanke and Oliver Keller.
+It can be used as an ab initio program, which means it bases its prediction purely on the
+sequence. AUGUSTUS may also incorporate hints on the gene structure coming from extrinsic sources
+such as EST, MS/MS, protein alignments and synthenic genomic alignments.
+http://augustus.gobics.de/binaries/README.TXT</readme>
+    </package>
+</tool_dependency>